[gmx-users] OPLSAA parameters

[friendli]

In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type 
opls_235 and opls_236.
While in oplsaanb.itp, the atom type opls_235 and opls_236 corresponds 
to atom "name"(as display in titles in oplsaanb.itp) C and O.

why there are two different "name"s for the same atom? what is the 
difference?

Qiang

Justin A. Lemkul wrote:
>
>
> friendli wrote:
>> Thank you Justin.
>>
>> Can you tell me how i can find the link between atom names and atom 
>> types?
>
> That is listed in the .rtp:
>
> ; name  type        charge    cgnr
>   CG    opls_235    0.500     3
>
>
>> The thing I wanna do is to figure out the bond parameters(b0,bk), and 
>> so the angle, dihedral parameters in oplsaa FF.
>> Is it possible to give me some examples, such as the bond between CG 
>> and OG1 in [ASN] in ffoplsaa.rtp?
>
> The easiest thing I can think of to do is use the -pp flag with 
> grompp, and look at the processed topology, which will explicitly 
> print the parameters.
>
> Otherwise, you have to interpret atom types from the .atp and apply 
> them to generic atom types in ffoplsaabon.itp (which can take quite a 
> bit of time!), so let grompp do the work for you, and use that as a 
> reference.
>
> -Justin
>
>>
>> thanks
>>
>> Qiang
>>
>> Justin A. Lemkul wrote:
>>>
>>>
>>> friendli wrote:
>>>> Dear all,
>>>>
>>>> To understand the exact parameters used in oplsaa force field, I 
>>>> read the ffoplsaa*.*** files.
>>>> But I can not find all the corresponding atom types in the 
>>>> ffoplsaa.rtp and ffoplsaabon.itp files.
>>>>
>>>> for example, in rtp file, there is a bond between atom type CG and 
>>>> OG1. But in *bon.itp, there is no such atom types CG or OG1 in the 
>>>> [bondtypes]. where is the bond constants etc kept? and how Gromacs 
>>>> find them?
>>>>
>>>
>>> CG and OG1 are atom names, not atom types.  The force field can 
>>> determine bonds based on atom types.  As long as they are recognized 
>>> atom types and parameters for such a bond are present, there will be 
>>> no problem.
>>>
>>> -Justin
>>>
>>>> Can anybody give a hint for this?
>>>>
>>>>
>>>> thanks in advance
>>>>
>>>> Qiang
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before 
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>
>>
>